Lista de obras - Akio Kitao - Dominio Público Uruguay

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method ⬇️

artículo científico publicado el 6 de febrero de 2013

An Efficient Timer and Sizer of Biomacromolecular Motions

artículo científico publicado en 2019

Binding free energy analysis of protein-protein docking model structures by evERdock

artículo científico publicado en 2018

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra

scientific article published on 29 November 2019

ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation

artículo científico publicado en 2018

Collective dynamics of periplasmic glutamine binding protein upon domain closure

artículo científico publicado en 2009

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space

artículo científico publicado en 1994

Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme

artículo científico publicado en 1998

CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

artículo científico publicado en 2013

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins

artículo científico publicado en 2009

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme ⬇️

artículo científico publicado el 1 de noviembre de 1998

Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton

artículo científico publicado en 2014

Detecting coupled collective motions in protein by independent subspace analysis

artículo científico publicado en 2010

Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model

scientific article published on 30 January 2019

Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes

artículo científico publicado en 2016

Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins

artículo científico publicado en 2020

Effect of solvent on collective motions in globular protein

artículo científico publicado en 1993

Effects of water model and simulation box size on protein diffusional motions.

artículo científico publicado en 2007

Energy landscape of a native protein: jumping-among-minima model

scientific article published on 01 December 1998

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

artículo científico publicado en 2010

Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method

scientific article published on 19 August 2019

Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment.

artículo científico

Erratum: "Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins" [J. Chem. Phys. 152, 225101 (2020)]

scientific article published on 01 November 2020

Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor

artículo científico publicado en 2019

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

artículo científico publicado en 2012

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method

artículo científico publicado en 2011

Functional Conversion of CPD and (6-4) Photolyases by Mutation

artículo científico publicado en 2016

Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor

artículo científico publicado en 2015

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility

scientific article published on 23 April 2019

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis ⬇️

artículo científico publicado el 1 de junio de 1994

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

scientific article published on 01 October 1995

High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments

artículo científico publicado en 2016

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

artículo científico publicado en 2020

High quality rendering of protein dynamics in space filling mode

artículo científico publicado en 2017

How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme ⬇️

artículo científico publicado el 1 de septiembre de 2003

Hydration affects both harmonic and anharmonic nature of protein dynamics

artículo científico publicado en 2008

Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

artículo científico publicado en 2008

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

artículo científico publicado en 2008

Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins

artículo científico publicado en 2019

Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.

artículo científico publicado en 1998

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

artículo científico publicado en 2013

Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding

scientific article published on 01 April 2020

Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation.

artículo científico publicado en 2009

Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations

artículo científico publicado en 2014

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

artículo científico publicado en 1997

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

artículo científico publicado en 2016

Molecular dynamics simulation of bacterial flagella

artículo científico publicado en 2017

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

scientific article published on 11 July 2019

Molecular dynamics simulation shows large volume fluctuations of proteins

scientific article published on 01 January 2000

Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase

artículo científico publicado en 2006

Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions

scientific article published on 01 August 2015

More efficient screening of protein-protein complex model structures for reducing the number of candidates

scientific article published on 29 November 2019

MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

artículo científico publicado en 2013

Multi-strand β-sheet of Alzheimer Aβ(1-40) folds to β-strip helix: Implication for protofilament formation

artículo científico publicado en 2018

Multidimensional replica-exchange method for free-energy calculations

Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulations

artículo científico publicado en 2009

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

scientific article published on 24 April 2007

Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins

artículo científico publicado en 2015

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

artículo científico publicado en 2018

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway ⬇️

artículo científico publicado el 21 de julio de 2013

Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7

scientific article published on 18 October 2019

Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation

artículo científico publicado en 2007

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

scientific article published in 2009

Protein boson peak originated from hydration-related multiple minima energy landscape

artículo científico publicado en 2005

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics

artículo científico publicado en 2017

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

artículo científico publicado en 2018

Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature.

artículo científico publicado en 2017

Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing

artículo científico publicado en 2011

Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases

scientific article published on 30 August 2018

Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus

scientific article published on 25 April 2019

Structure of the MotA/B Proton Channel

artículo científico publicado en 2017

Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism

artículo científico publicado en 2004

Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export

artículo científico publicado en 2010

Switch interactions control energy frustration and multiple flagellar filament structures

artículo científico publicado en 2006

TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P₂

artículo científico publicado en 2014

The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

scientific article published on 22 December 2011

The effect of end constraints on protein loop kinematics

artículo científico publicado en 2010

Thermal unfolding simulations of bacterial flagellin: insight into its refolding before assembly.

artículo científico publicado en 2008

Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding ⬇️

artículo científico publicado el 28 de julio de 2011

Universality and Structural Implications of the Boson Peak in Proteins

artículo científico publicado en 2019

Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins

artículo científico publicado en 2018

Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density ⬇️

artículo científico publicado el 24 de mayo de 2012

[Protein energy landscape and dynamics studied by molecular simulations and neutron scattering]

scientific article published on 01 July 2006

[Structure, function and self-assembly of the bacterial flagellum].

artículo científico publicado en 2005

[Universal joint of biological supramolecule: mechanism of bacterial flagellar hook investigated in silico]

scientific article published on 01 August 2005

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

artículo científico publicado en 2019

Lista de obras de Akio Kitao

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method ⬇️

An Efficient Timer and Sizer of Biomacromolecular Motions

Binding free energy analysis of protein-protein docking model structures by evERdock

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra

ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation

Collective dynamics of periplasmic glutamine binding protein upon domain closure

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space

Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme

CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme ⬇️

Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton

Detecting coupled collective motions in protein by independent subspace analysis

Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model

Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes

Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins

Effect of solvent on collective motions in globular protein

Effects of water model and simulation box size on protein diffusional motions.

Energy landscape of a native protein: jumping-among-minima model

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method

Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment.

Erratum: "Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins" [J. Chem. Phys. 152, 225101 (2020)]

Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method

Functional Conversion of CPD and (6-4) Photolyases by Mutation

Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis ⬇️

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

High quality rendering of protein dynamics in space filling mode

How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme ⬇️

Hydration affects both harmonic and anharmonic nature of protein dynamics

Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins

Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding

Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation.

Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

Molecular dynamics simulation of bacterial flagella

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

Molecular dynamics simulation shows large volume fluctuations of proteins

Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase

Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions

More efficient screening of protein-protein complex model structures for reducing the number of candidates

MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

Multi-strand β-sheet of Alzheimer Aβ(1-40) folds to β-strip helix: Implication for protofilament formation

Multidimensional replica-exchange method for free-energy calculations

Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulations

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway ⬇️

Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7

Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

Protein boson peak originated from hydration-related multiple minima energy landscape

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature.

Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing

Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases

Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus

Structure of the MotA/B Proton Channel

Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism

Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export

Switch interactions control energy frustration and multiple flagellar filament structures

TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P₂

The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

The effect of end constraints on protein loop kinematics

Thermal unfolding simulations of bacterial flagellin: insight into its refolding before assembly.

Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding ⬇️